nf-core_modules/modules/minimap2/index/main.nf
2022-02-04 09:53:32 +01:00

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process MINIMAP2_INDEX {
label 'process_medium'
conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' :
'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
input:
path fasta
output:
path "*.mmi" , emit: index
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
"""
minimap2 \\
-t $task.cpus \\
-d ${fasta.baseName}.mmi \\
$args \\
$fasta
cat <<-END_VERSIONS > versions.yml
"${task.process}":
minimap2: \$(minimap2 --version 2>&1)
END_VERSIONS
"""
}